3BD9

human 3-O-sulfotransferase isoform 5 with bound PAP

• PDB DOI: https://doi.org/10.2210/pdb3BD9/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-11-14 Released: 2008-01-29 
• Deposition Author(s): Xu, D., Moon, A.F., Song, D., Liu, J., Pedersen, L.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.249 
• R-Value Work: 0.203 
• R-Value Observed: 0.205 

Starting Model: other

Literature

Engineering sulfotransferases to modify heparan sulfate.

Xu, D., Moon, A.F., Song, D., Pedersen, L.C., Liu, J.

(2008) Nat Chem Biol 4: 200-202

• PubMed: 18223645 
• DOI: https://doi.org/10.1038/nchembio.66
• Primary Citation of Related Structures:  
  3BD9


• PubMed Abstract: 
  

  The biosynthesis of heparan sulfate (HS) involves an array of specialized sulfotransferases. Here, we present a study aimed at engineering the substrate specificity of different HS 3-O-sulfotransferase isoforms. Based on the crystal structures, we identified a pair of amino acid residues responsible for selecting the substrates. Mutations of these residues altered the substrate specificities. Our results demonstrate the feasibility of tailoring the specificity of sulfotransferases to modify HS with desired functions.

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Organizational Affiliation: 

Division of Medicinal Chemistry and Natural Products, School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.4 kDa 
• Atom Count: 2,202 
• Modelled Residue Count: 258 
• Deposited Residue Count: 280 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heparan sulfate glucosamine 3-O-sulfotransferase 5	A	280	Homo sapiens	Mutation(s): 1  Gene Names: HS3ST5, 3OST5, HS3OST5 EC: 2.8.2.23
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IZT8 (Homo sapiens) Explore Q8IZT8  Go to UniProtKB:  Q8IZT8
PHAROS:  Q8IZT8 GTEx:  ENSG00000249853

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A3P	B [auth A]	ADENOSINE-3'-5'-DIPHOSPHATE C10 H15 N5 O10 P2 WHTCPDAXWFLDIH-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.249 
• R-Value Work: 0.203 
• R-Value Observed: 0.205 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.27	α = 90
b = 59.27	β = 90
c = 173.957	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
StructureStudio	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-29 
Deposition Author(s): Xu, D., Moon, A.F., Song, D., Liu, J., Pedersen, L.C.

Revision History  

• Version 1.0: 2008-01-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.3: 2024-03-13
  Changes: Data collection, Source and taxonomy, Structure summary
• Version 1.4: 2024-04-03
  Changes: Refinement description
• Version 1.5: 2024-10-09
  Changes: Structure summary